Dear Hao In PyMOL bonds are essentially drawn based on a distance cut-off: Two atoms are considered bonded if
distance <= connect_cutoff + (vdw1 + vdw2)/2 You can generally adjust the sensitivity of bond recognition by adjusting the connect_cutoff global variable ( https://pymolwiki.org/index.php/Connect_cutoff ), eliminate a specific mis-assigned bond by using the unbond command unbond atom1,atom2 ( https://pymolwiki.org/index.php/Unbond ) or add a missed bond using the bond command: bond [atom1, atom2 [,order]] (https://pymolwiki.org/index.php/Bond) best regards Annemarie Honegger ____________________________________________________________ Dr. Annemarie Honegger Dept. of Biochemistry Zürich University Winterthurerstrasse 190 8057 Zürich Switzerland e-mail: honeg...@bioc.uzh.ch phone: +41 44 635 55 62 fax: +41 44 635 57 12 > > Today's Topics: > > 1. Unwanted bond formed in azetidine ring (Hao Li) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 3 Jun 2019 16:15:33 -0400 > From: Hao Li <hlum...@umich.edu> > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Unwanted bond formed in azetidine ring > Message-ID: > <calomrhqlgx3wn8jdzz09vt2n+x2j0o7hmfa1_jv_t9ogp2e...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear users, > > I am working on a structure of a protein-ligand complex, and the ligand > contains an azetidine group. Whenever I display this structure in pymol, an > unwanted bond forms between 2 carbon atoms in the azetidine ring. > > The pdb file of this ligand was generated by Chem3D and the restraint cif > file was generated by eLBOW in Phenix. I tried to edit both pdb and cif > files of the ligand but it did not work very well. I was able to remove > certain atoms but not the bond. > > I am kindly asking if there is a way to remove this unnecessary bond? Thank > you. > > Regards, > Hao > -------------- next part -------------- > An HTML attachment was scrubbed... > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: 20190603160708.png > Type: image/png > Size: 18310 bytes > Desc: not available > > ------------------------------ > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > > ------------------------------ > > End of PyMOL-users Digest, Vol 157, Issue 2 > *******************************************
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